{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T16:31:54Z","timestamp":1792168314524,"version":"4.4.0"},"reference-count":29,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,10,16]],"date-time":"2025-10-16T00:00:00Z","timestamp":1760572800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Immunol."],"abstract":"<jats:sec><jats:title>Objective<\/jats:title><jats:p>This study aims to investigate the potential role of B cells in the pathogenesis of Primary Sj\u00f6gren\u2019s Syndrome (pSS) by analyzing cell types, differentially expressed genes, and associated signaling pathways using single-cell RNA sequencing.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Peripheral blood mononuclear cells (PBMCs) from 3 pSS patients and 3 healthy controls (HCs) were collected. Single-cell transcriptomic analysis was performed, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, transcription factor analysis, pseudotime analysis, cell communication analysis, and B cell receptor (BCR) repertoire analysis. Genes and pathways potentially involved in the pathogenesis of pSS were identified, and key genes were validated by qRT-PCR. Statistical significance was assessed using T-tests and the Wilcoxon rank-sum test, with a p-value &amp;lt; 0.05 considered statistically significant.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Single-cell RNA sequencing of peripheral blood B cells from three patients with primary Sj\u00f6gren\u2019s syndrome (pSS) and three healthy controls (HCs) identified three subpopulations: memory B (Bmem), na\u00efve B (NaiveB), and plasma cells (PlasmaCells). In pSS, differentially expressed genes were enriched in Type I interferon signaling, antigen processing\/presentation, and MHC class II binding. Transcription factors related to interferon responses, including NR2F6, IRF5, STAT2, and IRF9, were upregulated. Cell\u2013cell communication analysis highlighted frequent interactions via TNFSF10\u2013TNFRSF10C and TGFB1\u2013TGFBR3. Pseudotime analysis indicated accelerated NaiveB differentiation along the effector branch. B cell receptor repertoire analysis revealed increased IGHV4-34 usage and higher IGHJ4\/IGHJ6 usage in PlasmaCells, with reduced IGHV1-3, IGHV1-69D, and IGHV2-7D usage. qRT-PCR validation in 22 pSS patients and 22 HCs confirmed significant ISG15 upregulation (p &amp;lt; 0.0001).<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>B cells contribute to the pathogenesis of pSS through the Type I IFN signaling pathway mediated by genes such as ISG15, alterations in BCR clonality, IGHV-J gene rearrangements, and abnormal gene usage.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fimmu.2025.1665086","type":"journal-article","created":{"date-parts":[[2025,10,16]],"date-time":"2025-10-16T05:31:42Z","timestamp":1760592702000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":7,"title":["B cell subpopulations and their role in the pathogenesis of primary Sj\u00f6gren\u2019s syndrome: insights from single-cell RNA sequencing"],"prefix":"10.3389","volume":"16","author":[{"given":"Xiaoyu","family":"Zhang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuanwei","family":"Han","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Song","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jia","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinhai","family":"Tian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinran","family":"Xin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bin","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Fang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hong","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,10,16]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMcp1702514","article-title":"Primary Sj\u00f6gren\u2032s Syndrome [J","volume":"378","author":"Mariette","year":"2018","journal-title":"N Engl J Med"},{"key":"B2","doi-asserted-by":"publisher","first-page":"16047","DOI":"10.1038\/nrdp.2016.47","article-title":"Sjogren syndrome [J","volume":"2","author":"Brito-Zer\u00f3n","year":"2016","journal-title":"Nat Rev Dis Prime"},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.1038\/nrrheum.2018.1","article-title":"B cells in the pathogenesis of primary Sj\u00f6gren syndrome [J","volume":"4","author":"Nocturne","year":"2018","journal-title":"Nat Rev Rheumatol"},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-023-06708-y","article-title":"Deconstruction of rheumatoid arthritis synovium defines inflammatory subtypes [J","volume":"623","author":"Zhang","year":"","journal-title":"Nature"},{"key":"B5","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1136\/annrheumdis-2016-210571","article-title":"American College of Rheumatology\/European League Against Rheumatism Classification Criteria for Primary Sj\u00f6gren's Syndrome: A Consensus and Data-Driven Methodology Involving Three International Patient Cohorts [J","volume":"69","author":"Shiboski","year":"2016","journal-title":"Arthritis Rheumatol"},{"key":"B6","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner[J","volume":"29","author":"Dobin","year":"","journal-title":"Bioinformatics"},{"key":"B7","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1186\/s13059-017-1382-0","article-title":"SCANPY: large-scale single-cell gene expression data analysis [J","volume":"19","author":"Wolf","year":"2018","journal-title":"Genome Biol"},{"key":"B8","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-019-0619-0","article-title":"Fast, sensitive and accurate integration of single-cell data with Harmony[J","volume":"16","author":"Korsunsky","year":"2019","journal-title":"Nat Methods"},{"key":"B9","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1038\/nbt.4314","article-title":"Dimensionality reduction for visualizing single-cell data using UMAP [J","author":"Becht","year":"2018","journal-title":"Nat Biotechnol"},{"key":"B10","doi-asserted-by":"publisher","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler: an R package for comparing biological themes among gene clusters [J","volume":"16","author":"Yu","year":"2012","journal-title":"OMICS"},{"key":"B11","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: kyoto encyclopedia of genes and genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"B12","doi-asserted-by":"publisher","DOI":"10.1038\/s41596-020-0336-2","article-title":"A scalable SCENIC workflow for single-cell gene regulatory network analysis [J","volume":"15","author":"Van de Sande","year":"2020","journal-title":"Nat Protoc"},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.1038\/s41596-020-0292-x","article-title":"CellPhoneDB: inferring cell\u2013cell communication from combined expression of multi-subunit ligand\u2013receptor complexes [J","volume":"15","author":"Efremova","year":"2020","journal-title":"Nat Protoc"},{"key":"B14","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4150","article-title":"Single-cell mRNA quantification and differential analysis with Census [J","volume":"14","author":"Qiu","year":"2017","journal-title":"Nat Methods"},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.4402","article-title":"Reverse graph embedding resolves complex single-cell developmental trajectories [J","volume":"14","author":"Qiu","year":"2017","journal-title":"Nat Methods"},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.1155\/2022\/4053038","article-title":"Epigenetic regulation of IFI44L expression in monocytes affects the functions of monocyte-derived dendritic cells in systemic lupus erythematosus [J","volume":"2022","author":"Luo","year":"2022","journal-title":"J Immunol Res"},{"key":"B17","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2023.1212330","article-title":"Exploring the shared molecular mechanisms between systemic lupus erythematosus and primary Sj\u00f6gren's syndrome based on integrated bioinformatics and single-cell RNA-seq analysis [J","volume":"14","author":"Cui","year":"2023","journal-title":"Front Immunol"},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2021.685837","article-title":"Type I interferon dependent hsa-miR-145-5p downregulation modulates MUC1 and TLR4 overexpression in salivary glands from Sjogren\u2019s syndrome patients [J","volume":"12","author":"Jara","year":"2021","journal-title":"Front Immunol"},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2008.06.008","article-title":"The nuclear orphan receptor NR2F6 suppresses lymphocyte activation and T helper 17-dependent autoimmunity [J","volume":"29","author":"Hermann-Kleiter","year":"2008","journal-title":"Immunity"},{"key":"B20","doi-asserted-by":"publisher","DOI":"10.1038\/ni.3212","article-title":"Guarding the frontiers: the biology of type III interferons [J","volume":"16","author":"Wack","year":"2015","journal-title":"Nat Immunol"},{"key":"B21","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1038\/nri3581","article-title":"Regulation of type I interferon responses [J","volume":"14","author":"Ivashkiv","year":"2014","journal-title":"Nat Rev Immunol"},{"key":"B22","doi-asserted-by":"publisher","DOI":"10.1002\/art.27223","article-title":"Genetic variants and disease-associated factors contribute to enhanced interferon regulatory factor 5 expression in blood cells of patients with systemic lupus erythematosus [J","volume":"62","author":"Feng","year":"2010","journal-title":"Arthritis Rheumatol"},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.1172\/JCI120288","article-title":"Inhibition of IRF5 hyperactivation protects from lupus onset and severity [J","volume":"130","author":"Song","year":"2020","journal-title":"J Clin Invest"},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.1002\/jbmr.3716","article-title":"Klf4 Promotes Dentinogenesis and Odontoblastic Differentiation via Modulation of TGF-\u03b2 Signaling Pathway and Interaction With Histone Acetylation [J","volume":"34","author":"Tao","year":"2019","journal-title":"J Bone Miner Res"},{"key":"B25","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa021933","article-title":"Development of autoantibodies before the clinical onset of systemic lupus erythematosus","volume":"349","author":"Arbuckle","year":"2003","journal-title":"[J]. N Engl J Med"},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.165.10.5970","article-title":"Disturbed peripheral B lymphocyte homeostasis in systemic lupus erythematosus [J","volume":"165","author":"Odendahl","year":"2000","journal-title":"J Immunol"},{"key":"B27","doi-asserted-by":"publisher","DOI":"10.1136\/annrheumdis-2012-202861","article-title":"Rheumatoid arthritis synovial tissue harbours dominant B-cell and plasma-cell clones associated with autoreactivity [J","volume":"73","author":"Doorenspleet","year":"2014","journal-title":"Ann Rheum Dis"},{"key":"B28","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1186\/s13045-017-0464-5","article-title":"Characterization and risk estimate of cancer in patients with primary Sj\u00f6gren syndrome [J","volume":"10","author":"Brito-Zer\u00f3n","year":"2017","journal-title":"J Hematol Oncol"},{"key":"B29","doi-asserted-by":"publisher","DOI":"10.1007\/s00428-022-03433-1","article-title":"Losing CD45 and various B-cell markers in a case of MYC-driven pediatric high-grade B-cell lymphoma, not otherwise specified that transformed from Burkitt's lymphoma during rituximab-containing treatments: a case report","volume":"483","author":"Xue","year":"2023","journal-title":"[J]. Virchows Arch"}],"container-title":["Frontiers in Immunology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2025.1665086\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,16]],"date-time":"2025-10-16T05:31:43Z","timestamp":1760592703000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fimmu.2025.1665086\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,16]]},"references-count":29,"alternative-id":["10.3389\/fimmu.2025.1665086"],"URL":"https:\/\/doi.org\/10.3389\/fimmu.2025.1665086","relation":{},"ISSN":["1664-3224"],"issn-type":[{"value":"1664-3224","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,10,16]]},"article-number":"1665086"}}